Homo sapiens smoking data (GSE68559)

Run parameters

Test	Expressioncutoff	Normalisation	Variancecutoff	Coexpression_measure	Edge_threshold	Threshold_method
GSE68559	1	upper_quartile	0.025	pidc	0.95	empiricaldistzero

Data preprocessing

Data cleaning

Before cut:

After cut:

Network construction

#manually copied from "/home/osbornejr/app/output/cache/GSE68559/expression_cutoff/20/normalisation/upper_quartile/sampling/0.025/similarity/pidc/sqrt_n/threshold/0.95/threshold_method/empirical_dist_zero"
# and  output/cache/GSE68559/expression_cutoff/20/normalisation/upper_quartile/sampling/0.025/
using WGLMakie,JSServe,Markdown,Graphs,GraphMakie,NetworkLayout,JLD2,DataFrames
Page(exportable=true,offline=true)
WGLMakie.activate!()
sample_file = "_assets/menu1/sample_counts.jld2"
adj_file = "_assets/menu1/adjacency_matrix.jld2"
sample_counts = JLD2.jldopen(sample_file) do file
    file["sample counts"]
    end
pre_adj_matrix = JLD2.jldopen(adj_file) do file
    file["pre-adj_matrix"]
    end
adj_matrix = JLD2.jldopen(adj_file) do file
    file["adjacency_matrix"]
    end
components = JLD2.jldopen(adj_file) do file
    file["components"]
    end
#Trim nodes with degree zero
    network_counts = sample_counts[components[1],:][vec(sum(pre_adj_matrix,dims=2).!=0),:]
#maintain list of vertices in graph
    vertexlist = copy(network_counts[!,:transcript_type])     
g = Graph(adj_matrix)
vertex_colors = replace(vertexlist,"noncoding"=>:red,"coding"=>:blue);

begin
	set_theme!(backgroundcolor=:white)
	fig,scene,p = graphplot(g;
		layout=Spring(dim=3,C=1.0),
		node_color = vertex_colors,
		node_size = 5,
		edge_color = :grey,
		edge_width = 0.1,
		figure = (resolution = (1500, 800),)
	)
	scene.show_axis =false
	fig
end

Network analysis

Network statistics

Nodes	Edges	Components	Nodes in largest component	Maximal degree
2466	94752	1	2466	153

Type breakdown

Step	Coding counts	Non-coding counts	Non-coding proportion
Raw counts	71709	32703	0.313
Clean counts	71688	32618	0.313
Sample counts	1793	816	0.313
Network counts	1694	772	0.313

Degree distribution

• All nodes:

• Coding transcripts:

• Non-coding transcripts:

Hubs

Nodes with degree \(k>\bar{k}+2\sigma_{k}\):

Nodes with degree \(k>70\):

Community detection

Community 1: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0031424	keratinization	2	2	0.13	0.0026
GO:0006656	phosphatidylcholine biosynthetic process	2	2	0.13	0.0026
GO:0007399	nervous system development	209	18	13.6	0.0034
GO:0042127	regulation of cell proliferation	127	14	8.26	0.0036
GO:0001649	osteoblast differentiation	23	4	1.5	0.0059
GO:0032206	positive regulation of telomere maintena...	3	2	0.2	0.0075
GO:0070198	protein localization to chromosome, telo...	3	2	0.2	0.0075
GO:0000122	negative regulation of transcription by ...	46	7	2.99	0.0075
GO:0019221	cytokine-mediated signaling pathway	31	8	2.02	0.0098
GO:0030593	neutrophil chemotaxis	9	3	0.59	0.0229

Community 2: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0000165	MAPK cascade	55	4	2.95	0.002
GO:0048011	neurotrophin TRK receptor signaling path...	36	4	1.93	0.014
GO:0043547	positive regulation of GTPase activity	9	2	0.48	0.022
GO:0003338	metanephros morphogenesis	6	3	0.32	0.026
GO:0001823	mesonephros development	13	3	0.7	0.026
GO:0048806	genitalia development	8	2	0.43	0.026
GO:0060054	positive regulation of epithelial cell p...	1	1	0.05	0.027
GO:0019800	peptide cross-linking via chondroitin 4-...	1	1	0.05	0.027
GO:0072287	metanephric distal tubule morphogenesis	1	1	0.05	0.027
GO:0033227	dsRNA transport	1	1	0.05	0.027

Community 3: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0033603	positive regulation of dopamine secretio...	2	2	0.17	0.0019
GO:2000065	negative regulation of cortisol biosynth...	2	2	0.17	0.0019
GO:0048484	enteric nervous system development	2	2	0.17	0.0019
GO:0032695	negative regulation of interleukin-12 pr...	2	2	0.17	0.0019
GO:0032348	negative regulation of aldosterone biosy...	2	2	0.17	0.0019
GO:0006941	striated muscle contraction	21	4	1.75	0.0054
GO:0048485	sympathetic nervous system development	3	2	0.25	0.0056
GO:0048208	COPII vesicle coating	3	2	0.25	0.0056
GO:0018279	protein N-linked glycosylation via aspar...	10	3	0.84	0.0078
GO:0051607	defense response to virus	16	4	1.34	0.0102

Community 4: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0016266	O-glycan processing	4	2	0.27	0.0056
GO:0050885	neuromuscular process controlling balanc...	5	2	0.33	0.0091
GO:1900181	negative regulation of protein localizat...	4	2	0.27	0.0310
GO:0030705	cytoskeleton-dependent intracellular tra...	9	2	0.6	0.0310
GO:0008045	motor neuron axon guidance	1	1	0.07	0.0315
GO:0042245	RNA repair	1	1	0.07	0.0315
GO:0015747	urate transport	1	1	0.07	0.0315
GO:0034063	stress granule assembly	1	1	0.07	0.0315
GO:0019885	antigen processing and presentation of e...	1	1	0.07	0.0315
GO:0006982	response to lipid hydroperoxide	1	1	0.07	0.0315

Community 5: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0008150	biological_process	1329	153	203.24	1.2e-06
GO:0035666	TRIF-dependent toll-like receptor signal...	9	6	1.38	2.0e-05
GO:0051403	stress-activated MAPK cascade	23	7	3.52	4.4e-05
GO:0002755	MyD88-dependent toll-like receptor signa...	10	6	1.53	4.7e-05
GO:0034138	toll-like receptor 3 signaling pathway	10	6	1.53	4.7e-05
GO:0034142	toll-like receptor 4 signaling pathway	11	6	1.68	9.7e-05
GO:0034162	toll-like receptor 9 signaling pathway	8	5	1.22	0.00017
GO:0034166	toll-like receptor 10 signaling pathway	8	5	1.22	0.00017
GO:0034146	toll-like receptor 5 signaling pathway	8	5	1.22	0.00017
GO:0038123	toll-like receptor TLR1:TLR2 signaling p...	9	5	1.38	0.00035

Community 6: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0008150	biological_process	1329	138	170.81	0.0012
GO:0055072	iron ion homeostasis	14	4	1.8	0.0015
GO:0001975	response to amphetamine	5	3	0.64	0.0037
GO:0006098	pentose-phosphate shunt	2	2	0.26	0.0056
GO:0033148	positive regulation of intracellular est...	2	2	0.26	0.0056
GO:0007512	adult heart development	2	2	0.26	0.0056
GO:0008272	sulfate transport	2	2	0.26	0.0056
GO:0090399	replicative senescence	2	2	0.26	0.0056
GO:0006915	apoptotic process	166	24	21.34	0.0098
GO:0055085	transmembrane transport	120	12	15.42	0.0152

Community 7: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0009235	cobalamin metabolic process	2	2	0.22	0.0037
GO:0060340	positive regulation of type I interferon...	2	2	0.22	0.0037
GO:0051988	regulation of attachment of spindle micr...	2	2	0.22	0.0037
GO:0071480	cellular response to gamma radiation	2	2	0.22	0.0037
GO:0006120	mitochondrial electron transport, NADH t...	7	3	0.76	0.0064
GO:0007059	chromosome segregation	18	6	1.96	0.0100
GO:0045670	regulation of osteoclast differentiation	5	3	0.55	0.0104
GO:0050715	positive regulation of cytokine secretio...	3	2	0.33	0.0105
GO:0035666	TRIF-dependent toll-like receptor signal...	9	3	0.98	0.0140
GO:0048011	neurotrophin TRK receptor signaling path...	36	6	3.92	0.0191

Community 8: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0034641	cellular nitrogen compound metabolic pro...	528	20	19.76	0.00049
GO:0033540	fatty acid beta-oxidation using acyl-CoA...	2	2	0.07	0.00061
GO:1901687	glutathione derivative biosynthetic proc...	4	2	0.15	0.00354
GO:0006805	xenobiotic metabolic process	16	3	0.6	0.00648
GO:0044281	small molecule metabolic process	239	12	8.94	0.00695
GO:0014047	glutamate secretion	8	2	0.3	0.01549
GO:0007283	spermatogenesis	40	4	1.5	0.01607
GO:0032504	multicellular organism reproduction	60	6	2.25	0.02297
GO:0070564	positive regulation of vitamin D recepto...	1	1	0.04	0.02495
GO:0060391	positive regulation of SMAD protein sign...	1	1	0.04	0.02495

Community 9: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0055085	transmembrane transport	120	12	8.39	0.0035
GO:0007596	blood coagulation	52	6	3.64	0.0038
GO:0035999	tetrahydrofolate interconversion	3	2	0.21	0.0044
GO:0006357	regulation of transcription by RNA polym...	126	6	8.81	0.0119
GO:0007269	neurotransmitter secretion	16	3	1.12	0.0137
GO:0032781	positive regulation of ATPase activity	5	2	0.35	0.0139
GO:0030049	muscle filament sliding	5	2	0.35	0.0139
GO:0001523	retinoid metabolic process	5	2	0.35	0.0139
GO:0051384	response to glucocorticoid	15	3	1.05	0.0185
GO:0042476	odontogenesis	19	4	1.33	0.0196

Community 10: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0008219	cell death	184	29	29.93	2.3e-06
GO:0008150	biological_process	1329	166	216.21	3.8e-05
GO:0006355	regulation of transcription, DNA-templat...	288	39	46.85	0.00034
GO:0051402	neuron apoptotic process	29	5	4.72	0.00269
GO:0007268	chemical synaptic transmission	71	14	11.55	0.00779
GO:0034501	protein localization to kinetochore	2	2	0.33	0.00806
GO:0021554	optic nerve development	2	2	0.33	0.00806
GO:0032463	negative regulation of protein homooligo...	2	2	0.33	0.00806
GO:0007080	mitotic metaphase plate congression	2	2	0.33	0.00806
GO:0015701	bicarbonate transport	2	2	0.33	0.00806

Community 11: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0010881	regulation of cardiac muscle contraction...	6	3	0.42	0.00089
GO:0007603	phototransduction, visible light	6	3	0.42	0.00131
GO:0048205	COPI coating of Golgi vesicle	2	2	0.14	0.00134
GO:0006890	retrograde vesicle-mediated transport, G...	3	2	0.21	0.00393
GO:0006891	intra-Golgi vesicle-mediated transport	3	2	0.21	0.00393
GO:0002027	regulation of heart rate	14	4	0.97	0.00617
GO:0086064	cell communication by electrical couplin...	6	3	0.42	0.00746
GO:0070933	histone H4 deacetylation	4	2	0.28	0.00766
GO:0051384	response to glucocorticoid	15	4	1.04	0.01013
GO:0001523	retinoid metabolic process	5	2	0.35	0.01247

Community 12: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0040015	negative regulation of multicellular org...	2	2	0.08	0.00051
GO:0051291	protein heterooligomerization	4	2	0.17	0.00295
GO:0007601	visual perception	14	3	0.58	0.00336
GO:0007568	aging	24	4	1.0	0.00391
GO:0060314	regulation of ryanodine-sensitive calciu...	7	2	0.29	0.00989
GO:0008217	regulation of blood pressure	21	4	0.88	0.01519
GO:0051603	proteolysis involved in cellular protein...	40	3	1.67	0.02216
GO:0034616	response to laminar fluid shear stress	2	2	0.08	0.02225
GO:0000302	response to reactive oxygen species	17	2	0.71	0.02243
GO:0007352	zygotic specification of dorsal/ventral ...	1	1	0.04	0.02278

Community 13: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0006099	tricarboxylic acid cycle	3	2	0.25	0.0057
GO:0035999	tetrahydrofolate interconversion	3	2	0.25	0.0057
GO:0030514	negative regulation of BMP signaling pat...	4	2	0.33	0.0111
GO:0007399	nervous system development	209	15	17.11	0.0126
GO:0001707	mesoderm formation	5	2	0.41	0.0179
GO:0008542	visual learning	6	2	0.49	0.0261
GO:0045668	negative regulation of osteoblast differ...	7	2	0.57	0.0355
GO:0008360	regulation of cell shape	17	3	1.39	0.0367
GO:0006367	transcription initiation from RNA polyme...	17	3	1.39	0.0367
GO:0050793	regulation of developmental process	169	15	13.84	0.0406

Community 14: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0008150	biological_process	1329	165	232.07	3.8e-05
GO:0006511	ubiquitin-dependent protein catabolic pr...	36	10	6.29	0.00022
GO:0072659	protein localization to plasma membrane	7	4	1.22	0.00070
GO:0007218	neuropeptide signaling pathway	13	5	2.27	0.00384
GO:0007267	cell-cell signaling	126	18	22.0	0.00437
GO:0007166	cell surface receptor signaling pathway	215	28	37.54	0.00693
GO:0071108	protein K48-linked deubiquitination	2	2	0.35	0.00796
GO:0042572	retinol metabolic process	2	2	0.35	0.00796
GO:0045672	positive regulation of osteoclast differ...	2	2	0.35	0.00796
GO:0030422	production of siRNA involved in RNA inte...	2	2	0.35	0.00796

Community 15: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0008150	biological_process	1329	47	59.82	0.0012
GO:0042059	negative regulation of epidermal growth ...	3	2	0.14	0.0019
GO:0000278	mitotic cell cycle	82	4	3.69	0.0249
GO:0042228	interleukin-8 biosynthetic process	2	2	0.09	0.0250
GO:0042267	natural killer cell mediated cytotoxicit...	4	2	0.18	0.0250
GO:0002495	antigen processing and presentation of p...	16	2	0.72	0.0252
GO:0030382	sperm mitochondrion organization	1	1	0.05	0.0255
GO:0048240	sperm capacitation	1	1	0.05	0.0255
GO:0042245	RNA repair	1	1	0.05	0.0255
GO:1900017	positive regulation of cytokine producti...	1	1	0.05	0.0255

Community 16: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0071280	cellular response to copper ion	2	2	0.2	0.0023
GO:0043691	reverse cholesterol transport	2	2	0.2	0.0023
GO:0006359	regulation of transcription by RNA polym...	3	2	0.29	0.0067
GO:0048013	ephrin receptor signaling pathway	4	2	0.39	0.0130
GO:0035329	hippo signaling	4	2	0.39	0.0130
GO:0010951	negative regulation of endopeptidase act...	12	4	1.18	0.0202
GO:0008219	cell death	184	13	18.06	0.0206
GO:0090263	positive regulation of canonical Wnt sig...	5	2	0.49	0.0209
GO:0007218	neuropeptide signaling pathway	13	3	1.28	0.0219
GO:0033138	positive regulation of peptidyl-serine p...	6	2	0.59	0.0304

Community 17: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0070098	chemokine-mediated signaling pathway	3	2	0.08	0.0010
GO:0006367	transcription initiation from RNA polyme...	17	3	0.47	0.0036
GO:0001570	vasculogenesis	6	2	0.17	0.0050
GO:0045669	positive regulation of osteoblast differ...	6	2	0.17	0.0050
GO:0035690	cellular response to drug	22	4	0.61	0.0061
GO:0060021	roof of mouth development	8	2	0.22	0.0091
GO:0001958	endochondral ossification	8	2	0.22	0.0091
GO:0010761	fibroblast migration	4	2	0.11	0.0185
GO:0003143	embryonic heart tube morphogenesis	7	2	0.19	0.0185
GO:0060548	negative regulation of cell death	81	3	2.24	0.0187

Community 18: Go annotation terms:

GO_ID	Term	Annotated	Significant	Expected	fisher
GO:0006112	energy reserve metabolic process	20	7	2.28	0.0013
GO:0048266	behavioral response to pain	5	3	0.57	0.0024
GO:0045672	positive regulation of osteoclast differ...	2	2	0.23	0.0042
GO:0010940	positive regulation of necrotic cell dea...	2	2	0.23	0.0042
GO:0051497	negative regulation of stress fiber asse...	2	2	0.23	0.0042
GO:0051056	regulation of small GTPase mediated sign...	39	7	4.44	0.0045
GO:2000134	negative regulation of G1/S transition o...	13	4	1.48	0.0118
GO:0019933	cAMP-mediated signaling	8	3	0.91	0.0119
GO:0071294	cellular response to zinc ion	3	2	0.34	0.0121
GO:0048873	homeostasis of number of cells within a ...	3	2	0.34	0.0121

3D visualisation

Graphlet counting

Comparing the typed representations of different graphlets in the real network to a set of networks with the same structure, but randomised node types.

• Tables

• Boxplots

Significantly overrepresented type representations

 



 

Significantly underrepresented type representations